We also used to have the same problem loosing beacon because of thunderstorms with an AL GPS2000 (Trimble). We do have two beacon stations that we are about half way in between and had the reciever set up so it would lock on to the strongest. The problem with that is if it switches stations sometimes the position would jump over a ways. The best solution for us was to fix the frequency to one station then if we started loosing the signal because of thunderstorms somewhere between us and the station switch it to automatic at that time and it would find the other station.

Three phase high voltage highlines will also wipe out the beacon signal (it is a low frequency AM signal) while underneath them.
Doesn't seem to affect WAAS.